These skulls could very well be the beginning of skull cults that would spread throughout the world and be found in other Neolithic sites. After all the site was visited by hunter-gatherers who did not remain at the site but continued on after visiting the site. There is nothing to suggest that the hunter-gatherers stayed long or settled in the area, so it is likely that they brought and expanded upon the traditions that were forged at Göbekli Tepe.
There is also another reason why the people who came to Göbekli Tepe would modify the skulls in order to display them. The skulls could have been those of enemies who had been dispatched and they were modified in order for them to stand out among the other skulls that would have been seen at the sight. The markings may have been part of a different ritual that was done to enemies over those who were allies. While this is an intriguing thought there is no way of knowing for certain without further evidence. More excavations at the site will hopefully turn up more clues for archaeologists trying to solve the puzzle.
The most likely scenario for at least some of the modification done to the skulls was for display purposes. The hole in one of the skulls may have been created so that the skull could be hanged as part of a display of numerous skulls. The mid line grooves on the skull may have also been an attempt to stabilize the skulls somehow as part of a display. As of yet large amounts of skull bones have not been found or examined so just how many skulls could have been displayed at the site and how long a skull would take residence at Göbekli Tepe is unknown.
There have also been statues and carvings found at the site that suggest there were rituals and a veneration of the human skull. One find has been a statue that was carved to represent a human and then the head was deliberately severed from the statue with some sort of tool. Another statue shows a head being carried as a gift to be presented to the temple. The final bit of artistic evidence at the site is a carving into one of the pillars that shows a bird-like creature missing its head.
Of all the bones found at the site that date from 10,000 to 7,000 years ago it is only these skull fragments that show signs of any sort of modification after death. The site had several pits that have animal and human bones mixed in with flint tools. It will take the discovery of new pits of further examination of the bones in the pits already discovered to definitively say what significance the skull held to the people of Göbekli Tepe and what rituals may have been performed at the site. It may also lead to greater understanding of why the site itself was created and where the people may have gone after the site was abandoned.